Changelog

0.4.0 — 15 October 2026

Pipeline

  • Added --max-aa to genome_entropy run (max_aa_len in run_pipeline), default 40,000. ORFs whose translated protein is longer are omitted and reported in a warning with their IDs. The ModernProst encoder builds a dense L×L mask, so a single pathological ORF call could exhaust GPU memory and fail the whole genome. On GTDB r232 this caused 39 genome failures, from ORF calls of up to 766k aa. 0 restores the old, unlimited behaviour. Output for proteins at or below the limit is unchanged.

0.2.0 — 17 August 2026

Structural-state analysis

  • Added raw per-ORF mutual information in bits between aligned 3Di and 12-state ModernProst representations. The schema is now version 2.2; legacy 3Di-only output remains compatible and reports the new field as null.

Fixes

  • Replaced stop-coordinate/C-terminal CDS matching with coordinate-normalised, strand- and phase-aware genomic overlap plus aligned translation comparison. Alternative starts, ambiguous X residues, small terminal differences, CDS-specific translation tables, codon_start, and missing translation qualifiers are now handled without unrestricted local matching.

Documentation

  • Audited repository documentation, public docstrings, CLI help, examples, and HPC templates against the current implementation.

  • Reconciled model identifiers with the live George Bouras Hugging Face namespace and documented current multitask versus deprecated 3Di-only models.

  • Documented 3Di and nullable 12-state output consistently, including the deterministic A–L serialisation.

  • Replaced automatic-normalisation guidance with raw JSON entropy and explicit downstream normalisation helpers.

  • Corrected coordinate, GenBank matching, ML splitting, missing-value, probability, device, and persistence descriptions.

  • Corrected the Read the Docs project name and aligned Python/tool version claims with package metadata and CI.

  • Made Sphinx warnings fatal in documentation CI and documented the local warnings-as-errors build command.

0.1.0 — 19 January 2026

Initial release with ORF discovery, translation, ProstT5 3Di encoding, raw Shannon entropy, modular CLI commands, JSON I/O, logging, batching, and device selection. Later releases added the unified schema, GenBank matching, ML, multi-GPU operation, and ModernProst/12-state support; those intermediate historical entries were not recorded in this file.